Hi I just found this thread and thought I'd give my opinion.
This interview is with Chris Haluke (Lead Designer for 343) on Jan 18 2013. In here he talks about the direction for season 2 so yes season 2 is confirmed. Release date however is not confirmed. If the link below doesn't work then google search: "Spartan Ops Season 2 Briefing" http://www.gametrailers.com/videos/w3oioy/halo-4-spartan-ops-season-2-briefing
Also late last year a member of 343 responded to a question about season 2 by saying "we'll see how season 1 goes". Which suggests that these spartan ops, although important, may not be 100% essential for halo 5. Of course there's some background story but it doesn't mean Halo 5 will continue with spartan ops material.
My opinion about season 2 is that the focus will be around Dr.Halsey. I personally don't believe Dr.Halsey will turn her back on humanity (although she's always cautious about UNSC). I've read all the novels and the Dr.Halsey diary that came with Halo Reach and I can say she's always been aware of certain members of the UNSC always trying to get rid of her. That's not new, so having an order to kill her shouldn't be much of a surprise. I think the much more likely scenario is that now she's been kidnapped, she used the "I want revenge" excuse to deceive Jul into thinking she's going to help him. Although she could really care less for the UNSC (even before the commander tried to kill her) she's always used them as a medium to get more knowledge. There was a theme throughout the spartan ops which shows how hungry Dr.Halsey is to learning about everything. Her character is also doings for the better of humans, although she usually won't do things to UNSC protocol she always has good intentions for mankind.
Anyway, I think Dr.Halsey will lead an attack with Jul onto the UNSC and seem like a villain throughout most of season 2, but only near the end she'll try to backstab Jul and steal both keys from the UNSC and Jul (or something like that). I also believe in this process both keys will be destroyed because really once either humans or covenant have both halves of the key, they basically won the war and will soon rule the galaxy. Since that's a cop-out way for the Halo story line to end, the key will likely be destroyed, maybe Dr.Halsey will come to a realization after stealing both keys that it's too dangerous to let anyone have it (both UNSC or Jul) so she'll decide to destroy the keys and would involve killing herself as well.
Anyway the real reason why I believe this is because I don't think there can be any mind blowing changes that happens during the spartan ops for 2 reasons:
1. There was a chance season 2 wouldn't happen so how important could the story be? I'm sure they already have the story outlined for Halo 5 and 6
2. Spartan ops is not essential to following the Halo Reclaimer trilogy. Just like the rest of the halo fiction (novels, comics, etc.) they're never essential to understanding the stories in the game but give a really good background story. The games should be able to stand alone though as most halo fans don't follow the other fiction in this universe.
Sorry for the long message but just to add something. I don't believe cortana is dead. I mean we know that in spartan ops Dr.Halsey received 'memories' from the attack on new pheonix which could mean the AI the index created out of modern humans were cataloguing itself. This is an important point because where did Cortana die? She died in the index, which is a weapon that converts humans into AI that'll be given a body. I seems likely that Cortana may come back in Halo 6 (not Halo 5 as that's too early) as a real being.
Only time will tell and I could very well be completely wrong but these are my thoughts.
